Family Trees
by redfox1303
Summary: Five years have passed since Scully gave up her son for adoption but now after the unexplained death of his adoptive parents, the FBI has taken William into custody for his safety. Looks at the events following this incident and the difficult relationship between M&S and their son as they try to protect him once more
1. Chapter 1

_Five years have passed since Scully gave up her son for adoption but now after the unexplained death of his adoptive parents, the FBI has taken William into custody for safety. Looks at the events following this incident and the difficult relationship between M&S and their son as they try to protect him once more _

_Disclaimer: I do not own the X files or the characters, I'm just borrowing them._

The house in the countryside had been their safe haven for over a year now. It was a crisp November morning and a figure was out jogging along the frozen footpaths. Special Agent Mulder was strict with his keep fit regimes. He always had been, even on a snowy winter's day. In fact, Mulder often preferred such temperatures. The burning and simultaneous numbness across his body was exhilarating. Mulder pushed his way through the heavy gates of their front garden. His grey sweat pants had soaked around the ankles making his feet bitter cold.

Inside, Scully was busy at work writing out notes on a seminar she had to deliver later next week.

"How's it coming along?" Mulder asked unzipping his hoody.

Scully sighed leaning back in her chair. "Fine; how was the run?" She caught sight of the slushy muck he'd trailed in on the carpet and threw him a look.

"Oops, don't worry I'll clear it. Coffee?" he darted into the kitchen to escape.

Scully was stressed. Becoming a doctor had been her dream; the problem was that she was determined, too determined in fact, which meant she took every case home with her. Detaching herself from the x-files had been easier than this job. It was beginning to take its toll.

"Listen, I've got to go to work this afternoon, I'll only be a couple of hours, I just need to catch up on some bits" Scully often went above and beyond the requirements of her work.

Mulder appeared with two steaming drinks in hand. He kissed her forehead softly. "Okay" he replied flopping out on the nearest coach, "I'll make dinner for when you get home".

The front door closed and Scully locked it behind her. Mulder listened to the car engine as it pulled out of the driveway and set off up the lane. He was alone and in silence. For the past few weeks he'd been bored out of his mind. He'd always kept close tabs on any news of the colonization but for a while things had been very quiet.

This extra-terrestrial world had been his passion, his mission; and he'd devoted so much time and energy into it. He was reaching burnout. They both were. Of course, he loved Scully to bits, she was his world now, but he missed the old days back in DC chasing monsters and bad guys together. Scully had been suffering recently; she'd never quite gotten over William, how could any parent get over losing their child? Mulder wished he could give her what she truly wanted, but he knew it was never meant to be.

The phone rang and Mulder had to search around for it - stupid cordless thing kept getting left in strange places; admittedly mainly by him.

He unraveled it from the throw rug on the coach, "Mulder" he answered, forgetting he wasn't supposed to use his real name.

There was a delay before the voice spoke down the other end of the line; Mulder recognized it immediately. He'd not heard from this man in far too long.

"Walter Skinner?!"

"Yeah, Mulder, it's me, we need to talk; it's about your son"

Mulder collapsed into the coach. If Skinner was about to tell him the bastard colonists had found William he wasn't sure what he'd do. How on earth would he tell Scully that her son, whom she gave up to protect, had been taken?

"There's been an incident; can you and Scully meet me in Maryland?" Skinner asked.

"Is he alive?" Mulder held his breath.

"Yes, he's alive. Listen, I don't know what you're going to tell Scully but I realize this is difficult for the both of you"

As soon as Skinner had hung up the phone, Mulder had pulled the duffel bags from storage and began filling them with his and Scully's clothes; he'd pick her up straight from the hospital. How was he going to explain to her that he'd asked Skinner to keep an eye on William all these years; would she think lowly of him for keeping this from her? He feared it would re-open a lot of painful wounds for Scully; for them both.


	2. Chapter 2

The agents had been on the road for nearly two hours now heading east to Maryland. Outside the car it was turning to night and the stars were starting to peak through clouds. They both wore thick jackets as the cars air con had been broken a while; a job that had been on Mulder to do list for over six months.

Scully sat looking straight through the windscreen; she was in shock, unable to comprehend what her lover had just revealed. The only noise came from the faint rumble of the vehicle gliding along the dirt tracks.

"How did they find him?" She spoke slowly, to herself as well as Mulder. They'd done everything they could to protect him and it wasn't enough.

"I don't know, but he's safe and in good hands, that's all that matters right now"

Mulder had no idea what they'd do once they got to him. The word 'safe' no longer existed. It would be too dangerous to re-enroll William into social services; if they found him this time, they'd find him again. What still bothered him was how William had survived. From the vague explanation Skinner had provided it sounded like the murderers had died along with the adoptive parents. Miraculously the only survivor was William.

They pulled in at the gas station just up the road to fill up; they'd been running on fumes the last couple of miles. Mulder wrestled the hand-break and got out to sort the pump. Scully didn't move the whole time. Her face almost had a glazed expression.

Mulder heaved himself back into the 4x4 and placed a handful of candy bars and chips on the dashboard.

"Mulder" Scully's eyes looked as though they were holding back tears "It's been five years; this is our son, Mulder, our boy, and he's not going to have a clue who we are…"

He squeezed her hand tight in his. This was destroying Scully inside; he questioned if he was right it letting her know at all, perhaps he should have dealt with the situation alone to spare her this turmoil.


	3. Chapter 3

It was early hours of the morning when they finally arrived at the secure house in Maryland. Skinner was there waiting for them with two other armed agents for protection. Everything had been done off the records, Skinner had made sure of it. The last thing they needed was the FBI capturing Mulder.

"Where is he?" Scully asked calmly. He gestured to one of the back bedrooms. The door was pulled to but not entirely shut so that the landing light seeped in. Bundled up under the covers somewhere inside that room was William Mulder. The other two trusted agents of Skinners were in the lounge and kitchen keeping watch.

"We've got all of his files; everything is here, the last hard copies of his existence. We've cleared everything from the social services, schooling, and medical databases. He's a ghost"

Scully felt a lump in her throat. She was ashamed that her William had to become the same as them, a nobody who lurked in the shadows. She'd wanted so much for him to have a normal life.

Mulder picked up the brown paper file. Inside was a photograph; the first picture either of them had seen of their son. It was one of those professional photo prints with a cheesy fake backdrop. Mulder had half expected to see thick auburn hair, but instead the boy looking back at them had medium brown, very similar to his own. The grin on the boy's face reminded him of Samantha when she was younger; perhaps there was a bit of her in him. He saw Scully's eyes in him too. He was there son, without a doubt.

It was strange; up until now William had been a baby to him, he'd always remembered him as a rather helpless and boring poop-machine, a loveable one nonetheless, but totally dependent on Scully and him. Now, William was a little person, he'd have his own personality, sense of humor, likes and dislikes.

"Yesterday evening local law enforcement got a call out about a domestic disturbance. Gun shots were fired. When they turned up they found four bodies and William, who was unharmed. The bodies of William's adoptive parents, Annemarie and Thomas Barnes were found in the front room with gunshot wounds to the chest and head. The other two bodies cannot be identified"

"Bounty's" Mulder cut in; he'd already guessed they'd be the ones behind this, yet they hadn't managed to kill William, there target. It didn't make any sense. Scully hadn't looked up from the photo.

"Obviously there are a lot of questions that need answering. I think it's best if you two get some sleep and then we can tackle things in the morning, decide what the best arrangement is and press forward with the case"

Mulder sensed Scully flinch. He knew she wanted to see William now.

"Come on, Dana" he kissed her forehead and let Skinner point them in the direction of a free room. Tomorrow they'd meet their son. Tonight they'd let him sleep.


	4. Chapter 4

Mulder woke gradually to Scully caressing his arm with her fingertips. He caught a glimpse of the alarm clock in their foreign bedroom; 5am, they'd only been asleep a few hours. Mulder rolled over to face his partner.

"Can't sleep?" he asked rather mindlessly; she'd clearly not slept a wink. "Do you want to talk?"

Birds were stirring outside but inside the house was silence. It felt like staying over an unfamiliar relative's house. This room was a lot smaller than the one back at the house in the country. It didn't feel quite as bitter cold down here though.

"Mulder, I don't know what to say, I'm sorry, I just want to see our son. I want him back with us but I don't know how it can possibly work like that"

Skinner and Mulder were sat at the kitchen table with a mug of steaming coffee each. Mulder was busying himself with the paperwork and catching up with life with Walter. Scully was hidden away in the bedroom tidying herself up a little.

"So did anyone question William when the police got to him, did he say what had happened?" Mulder asked.

Walter took a sip of his coffee and shook his head, "Nothing, he just said he couldn't remember, seems pretty shell shocked, as any kid would be after witnessing something like that"

Mulder was sure Scully would want to check William over before anything else went ahead. Poor kid would have probably been traumatized by the whole thing, he'd likely need therapy. Something caught Mulder's eye on the files he was flicking through. Epilepsy, nosebleeds, he'd been emitted to various child psychologists over the years too.

"There's child abuse flagged up on his record" Mulder scanned through the next page rather surprised. The pictures of marking all over William's body were recognizable instantly to Mulder; signs of abduction. How could this be?

"The parents insisted they never touched him; no evidence could be found to prove it was them. These marks weren't done by any human abuse; they're trademark abduction scars, unmistakable"

Scully entered the room just in time to hear Mulder's theory.

He handed her the files across the table "Tell me you've seen those before, Scully"

She took the documents and her heart sank instantly. It looked like they'd taken him multiple times by the state of his frail little back and stomach; they were bruised dark purple with occasional small red branding. She wondered if they stuck implants in young ones too.

"Mr and Mrs Bennett must been distraught when they found there son had been made to looking like that" Skinner added.

Both Mulder and Scully certainly felt very distraught after seeing the pictures. Mulder couldn't help feel his throat tighten. It was bad enough these extra-terrestrials had abused him and Scully but to hurt their six year old boy was infuriating at the thought.

The wooden door creaked open from William's assumed bedroom. The boy wandered across the hall and into the bathroom without giving the adults at in the kitchen a glance. He'd no Pajamas with him just yet as they had to remove him from the house pretty quickly amongst all the chaos. Instead he slept in his underwear and a t-shirt. He sported some wacky morning-hair which Scully noticed resembled Mulder's 'just-woken-up' look.

Mulder found Scully's hand under the table and held her for reassurance. Things would be alright.


	5. Chapter 5

One of Skinner's agents appeared at the front door, he was holding bags of William's things collected from the old house, which had now been closed as a crime scene.

"Do you want those put in your car now or later?" Skinner asked both Mulder and Scully.

Realisation hit them. They would be taking William home with them. It was the most logical thing to do, the safest thing by far, besides the boy should be with his real parents. Mulder panicked slightly. He'd not quite adjusted himself to the idea of a family. He loved his life with Scully and the lack of responsibility; a child would change everything, perhaps they weren't ready for this?

The sound of a muffled chain flushing came from the other room and William made his way into the kitchen. The boy looked at the adults in front of him; he stood rather awkwardly not quite knowing what to do with himself. He'd only met three of these men yesterday and now there was another unfamiliar man and a lady.

Scully was overcome with emotion. Her precious baby boy whom she remembered as a babbling one year old had grown into such a gorgeous child.

"Hello, William" Scully managed.

"Hi" came a shy and quite reply.

The boy's life had been thrown upside down in such a short space of time. He'd woken up this morning and for an instant believed he was in his own room, and that nothing bad had happened. As he rubbed his bleary eyes, the consciousness returned to him. His parents were dead, and he was alone in the world.

The agents fixed him up with some cereal and William took himself off to the lounge, plonking himself in front of the television.

"I've got this place until this evening, after that you'll need to leave. I'll handle the reports and keep the press out of the way, as far as neighbours and relatives are concerned, William Bennett has been anonymously rehomed through another adoption agency. Will you both be alright with the boy?"

"Of course, he's our son" Scully defended.

"I meant no offence. I just know how strange a situation this is for everyone; no one was expecting this. If you need time to talk things over - ?"

Mulder could see Scully ready to jump in with an answer. He rose from the kitchenette and gestured Scully towards their room. He needed a moment with her alone, before they all got ahead of themselves.

Once inside Mulder pulled the door to. He'd run through their options in his head. Either they took William in, or he remained in the custody of child protection until they could find a securer family. They needed to think clearly before jumping to conclusions.

"Scully, this is emotional for all of us, it's all happened so fast and I think we need to stop and take a look at the bigger picture, discuss things, together"

"What is there to discuss? He's our son, we'll make it work" she fought.

"But Scully, look at our life, you said it yourself, it's dangerous; besides I don't know a thing about being a parent" Mulder was on the defensive, and not entirely sure why. Was this his self-preservation instinct kicking in as he feared such a dramatic change to his lifestyle, why was he so reluctant to keep his son?

"Well, we are parents, we'd better learn quickly" Scully felt betrayed by her lover. Hurt that he could think in such a way. She'd spent five years apart from her William; and cried so many tears in that time. For five years she'd blamed herself. She imagined him growing up, his second birthday as he became a toddler; his first words, his first day at school. She'd missed so much of his life. Tears filled her eyes.

Mulder realised what all this was doing to her. He felt guilty for reacting the way he had done, so inconsiderately towards his partner. He pulled her into a hug and held her tight, wrapping her up in his arms.

"Honey, I'm sorry" he spoke as he kissed her head softly.

"I just… I can't believe this is happening, and I'm not ready for it either, Mulder, but I know God has brought us back to William for a reason. I can't let him go again"

Mulder nodded, "I know what this means to you, it means a lot to me too, and I guess I'm just a little scared of being a father. The darkness finds us, Scully, always; I just hope we can keep it away for long enough to raise this child"

The pair sat on the bed for a while, both trying to recompose themselves.

"If we agree to take him, we need to both be fully committed to this, it's never going to work unless this is what we both truly want" Scully wiped her eyes and sat upright. She had to give Mulder plenty of time to make this decision. He was a nomadic individual, he followed the phenomenon; raising a child was vastly different from chasing monsters in the dark, which was all he knew up until now.

"I'm not sure I'm ready to be a father, but I am ready to try and learn to be one. I do want this with you, Scully. I think we should take our son home"


	6. Chapter 6

It was later in the day and the agents were working out logistics. Skinner was busy on the phone whilst Mulder was looking into the report evidence at the crime scene and coronary write ups. William's survival made no sense and he still seemed to remember nothing. Had there been another involved in the incident? Somebody that stopped the bounty hunters from completing their mission, and if so, where was that individual now? Then again, William had always been a special boy, right from birth. Mulder remembered Scully telling him how their son had levitated a piece of metal work above his crib, hovered it delicately above his head. Was there something else behind all this?

William was sat at the kitchenette along with one of Skinner's agents who was supposedly keeping the child entertained. The man held a pack of cards rather smugly dealing them between hands. His little icebreaker magic tricks worked with his mates down the pub, it would surely impress a snot-nosed kid.

William slouched over the marbled counter top with his chin buried into folded arms. His eyes watched intently as the strange man flicked the cards quickly and then laid them out in a fanned shape on the counter. Scully entered the kitchen; she'd just got off the phone with her mother. She rucked the sleeves up on her sweater, it had been frosty outside and the chill had followed her in. She watched her son closely wondering if he still had traces of the alien tendencies; could he read minds like Gibson Praise?

The agent looked gobsmacked as William pointed out the obvious to him, totally ruining the act. The boy was innocent enough, just totally un-fooled by the charades.

"Is he counting cards already?" Mulder joked quietly to Scully, although he too was a little concerned with mind-reading.

"I saw you put it up your sleeve" William pointed out.

The two parents breathed a sigh of relief, "No, he's just observant" she smiled.

Skinner finished up on the phone and pulled the agents aside. He suggested they try talking to William once more about yesterday's events. Any answers might give them some leads and help gauge just how much danger William was still in. They decided to migrate to the lounge to discuss things privately. Mulder and Scully sat together on the large fabric couch and Skinner stood behind them, more of an observer. Little William was perched on one of the single armchairs facing the three adults.

"William, can you tell us what happened the other day at the house?" Mulder began.

The boy contemplated for a while, he felt awkward looking at them so instead fiddled with the remote in his hands. He shook his head. Maybe they'd leave him alone if they knew they'd get nothing out of him. After all, he didn't remember much at all anyway, only figures and shouting.

"You don't want to tell us, or you can't remember?" Mulder probed.

"I don't remember it" he mumbled, still refusing to make eye contact.

"Can you tell us what you do remember, before it happened?"

William scrunched up his face, trying hard to picture it. Snippets played back through his mind, and he narrated it as they came.

"I was in bed; I had a bad dream so I went downstairs. There were some people at the door and my Daddy was talking to them" he explained slowly.

"And then what happened, William?"

"Nothing, I don't remember anything else" the boy was lost in thought.

He hurt inside, knowing he'd never see his family again. He was frightened and unsure of what was to come. The only certainty was the constant and intense feeling that something bad was still to come, a dread of impending doom. He felt particularly strange towards the man and woman, the woman more so than the man; as though he knew them well, he'd always known them. Maybe they were an old friend of his parents that he'd occasionally met when growing up, but the connection felt stronger than just that. It was weird.

Mulder knew what they had to do; it was the only thing that might get them some answers and they needed to act fast whilst things were still fresh in the mind. He expressed to Skinner and Scully the need for hypnotic regression therapy. If they found one today before they took William home with them it might be the last chance for clarity. Scully felt immediately reluctant, she was adverse to the effectiveness of such methods anyway, but she had to admit it had helped them in the past with the X files on a few cases. Eventually everyone agreed to the idea. They'd ring around and set off shortly.


End file.
